When You Were Gone
by MisfitQueen
Summary: Blossom is presumed dead after the Puff's home is completely trashed. The Professor is no where to be found. Everyone in town seems to be against the remaining Puffs. The only ones who they can turn to is the Ruffs who are just as heartbroken. It's up to them to figure out what happened and to find Blossom and The Professor... If they are still alive.
1. Chapter 1

" _ **Everyone keeps telling me that time heals all wounds, but no one can tell me what I'm supposed to do right now. Right now I can't sleep. It's right now that I can't eat. Right now I still hear his voice and sense his presence even though I know he's not here. Right now all I seem to do is cry. I know all about time and wounds healing, but even if I had all the time in the world, I still don't know what to do with all this hurt right now."**_ **  
** _ **― Nina Guilbeau, Too Many Sisters**_

* * *

 _When was the last time that I told you I loved you?_

"Shh." Blossom placed her hands on both mine and Bubbles' mouth. I can still smell her Sweet Pea lotion. Taste it even. She had moved so quickly that my teeth grazed her soft palms. But… she was distracted.

Bubbles and I didn't dare to move. Usually, one of us would let our curiosity get the better of us. We would question her, or at least take her hands away so we could look for ourselves. Though, when we looked at each other, we knew this time we would have to listen.

Her voice was sharp and commanding. Not like when she was just barking orders, or just being naggy about chores. There was something laced in her words. I hate to say it, but it was fear. Blossom was afraid of something. That was why we didn't move. That is why Bubbles and I just watched her face and look to each other. Blossom wasn't one to just get scared.

I felt my breath hitch in my throat when she looked at us. Desperation. Urgency. Complete and utter terror. Her eyes were glazed over with these and more.

"Get up." She whispered. Her hands had moved from our mouths to our arms, picking us up. Without any more words, we let her lead us to our closet. Our eyes widen when we saw what she had in mind.

The secret door. It was a small bunker the Professor designed for emergencies. It was made of titanium on the inside and held canned rations for long stay periods. There was even a small bed at the bottom. Never in my life did I expect to ever use it for anything other than hide and seek.

"Bloss-"

"Shh." Blossom interrupted Bubbles. I could see the prominent fear in Bubbles' eyes. She even had tears falling down her cheeks. Blossom quickly wiped her cheek and kissed it. "Get inside and do not open it for any reason. Promise me." She spoked sternly as she pushed us down the bunker. I saw her make no move to join us.

"What about you?" The question ripped from my throat.

"Promise me." She demanded. I could hear Bubbles sob below me. I could feel my own eyes burn. I nodded my head no longer able to talk. I felt her finger caress the side of my face. "I love you both so much." She kissed my head, trying to push me further into the bunker.

Then she closed the door. I locked it immediately, not needing Blossom to command me any further. I grabbed a hold of Bubbles and clung to her. She shook violently in my arms and sobbed as quietly as she could. We both knew what this meant…

And the result… We would probably never see our sister again…

 _I love you too!_

* * *

 _Three Days Prior_

"Yes Mayor." The sound of Blossom's voice gained my attention. I had just walked out of the bathroom and was heading back to my own room when I heard her. "Of course, I will look into it immediately." I can't really explain it… but it was one of those feelings that made the hair on your neck stand up that consumed me. A kind of passive fear that entered my body.

I peeked in her room and saw that her back was to me. Her left hand held the hotline to her ear as her right hand was up to her mouth. It was a quirk Blossom had when she was worried. She will just rest her hand right on her chin almost as if she's about to cover her mouth.

"I would rather not. Buttercup and Bubbles don't need this type of burden I their lives. Buttercup has soccer and track, while Bubbles has Cheer and Tennis. I will handle this on my own." She paused as she listened to him speak. "No. Honestly it's not a bother. I'm actually glad you brought this to my attention, though I doubt it's as bad as it seems. I just need to do a routine report and have it cleared."

Now I was really curious. This had to something much bigger than she was letting on. Blossom had her own after school things to do. This thing had to be something pretty bad in order for to keep it from us. I trust my sister with all my heart, but sometimes she's too independent for her own good.

"Thank you, Mayor. Have a nice day."

I quickly walked away to my room. I closed the door softly and walked to my desk and turned the lamp on. In a matter of seconds I heard knocking on my door. I knew who it was, but I still had to play it cool.

"Who is it?" I called out, quickly tapping my password into my laptop. Thankfully, I already had a video on YouTube paused. That way she wouldn't second guess what I was doing.

"It's just me." Blossom said entering my room. I pretended that I had just paused my video, and looked over at her. She sat behind me on my bed and just plopped down.

You know, Blossom and I fight all the time. We cuss and scream. Hell, we have even throw some punches or two, but she was my best friend. Not to say that I wasn't close to Bubbles. But that girl is too much of a damned social butterfly. She had too many of her friends' issues running through that blonde head. She would never understand what I said like Blossom does. I could just grunt and Blossom would know what I meant. (It's been proven)

Seeing her just lay on my bed wasn't strange. In fact, we alternate rooms half the time. To think, I was the one who teased Bubbles relentlessly for missing our old shared room, when it was me who missed the closeness. Though, no one could ever make me admit it.

"You good?" It was kind of a probe question. This would be her chance to tell me. There were hardly any secrets between us. And those few that we do have are for important reasons.

"Just exhausted. Brick kept messing with me all day and then Butch kept putting his finger in my ear during History. The only class I don't have Brick."

Ah, The RowdyRuffs. Now that's a story.

Five years ago, when we were twelve, we had just gotten a call on the Hotline. The Ruffs were robbing a video game store… or so everyone thought. You see, the Ruffs went missing for about five years. We figured they just got bored and moved to new territory. So when we heard they came back, we were wary. Though, turns out they had caught three teens stealing the games and were returning them. The clerk had been scared, however, and reported them as the thieves. We would have believed him to if it weren't for the fact that they didn't resist. No kicking. No punching. No name calling. Nada.

They had told us that they were tired of being blamed for things that went wrong simply because they breathed the same air. They felt like monsters. It hit a chord in us considering that's how everyone viewed us at first.

Surprisingly enough, Blossom was the first to believe in them. She invited them to stay with us until future arrangements could be made. The Professor didn't argue. He believed in our word. It was only a matter of days before Miss Keane came and took them in.

Even though, they're not evil… doesn't mean they're still not annoying.

Butch has been a pain in my side ever since. He's always flirting with me and being obnoxious. Boomer is like a baby duck. He follows Blossom and I around constantly. Unless Bubbles is around, then he's always at her side. Not that she minds. Bubbles loved having a new play buddy. Brick, unless you had long red hair and bright pink eyes, he didn't even acknowledge your existence.

They are good friends though. Butch is always there helping us out. He's protective over Blossom and Bubbles when it comes to other guys hitting in them, and Boomer is like a little brother I've always wanted. Just the soft-skinned kind. Blossom and Bubbles love to have him help them cook. He doesn't complain though. Brick and Butch usually are the ones I hang out with when it comes to sports. More Butch then Brick. Like I said, he's only interested in annoying Blossom and competing with her.

Getting under her skin is his favorite hobby.

She sighed heavily from her spot. I wouldn't have been surprised if she was about to fall asleep. Blossom worked hard every day. She was our Student Body President, President of the school's choir, and President of the yearbook staff. That was just academic responsibilities. She had even more to do that was for civilians in just day to day life. Not to mention all the things she did for Bubbles and I.

"Sometimes… I wish I could just run away." I heard her mumble. I chuckled turning my chair back to my desk. I looked down at my laptop opening the FaceBook tab and logging in. I rolled my eyes when the first thing that popped up on my feed was Butch and his stupid abs selfie.

"Your sense of responsibility won't let you do that." I spoke up. I heard her grumble which made me smile bigger. Sometimes it was refreshing talking to my sister instead of my boss or leader.

"I know." She groaned. Then I saw her sit up from the corner of my eyes. "I'm going out to run an errand for the Mayor. The Professor won't be home until tomorrow night. You and Bubbles might think about going to Miss Keane's and having dinner with her and the boys."

"Okay." I said. "Anything special?" Another probe question. She looked down, another quirk of hers. She was hiding something.

"No. Just simple running around, but it is time consuming." I nodded, accepting the answer. We only keep secrets for good reasons. She'd tell me when the time came.

"So… what should I tell your boyfriend. He'll be heartbroken to know you won't be eating with us." I smirked. Her head snapped up. Her cheeks were puffed up.

"Brick is not my boyfriend." She gritted out.

"I never said Brick, now did I?"

"Ugh! You're such a pain, sometimes!" She yelled stomping out y room. I laughed spinning in my chair.

"I love you too!"

 _I loved you so much, Bloss. I'm sorry._

* * *

 **Thank you everyone for taking your time to read my newest story. I think what I need is a new motivation in order to continue with some of my other works.**

 **Again, I have a warning on this story due to getting into emotional events that may be too much for some readers. I focus on family and friend bonds so you will be seeing a lot of the emotional turmoil that will happen when something threatens such bonds.**

 **All pairings are original: Reds, Blues, and Greens. I feel I have to put that out there before any confusion sets in. If you have read my other story you will know that I love exploring the dynamic relationships of the characters. Blossom and Boomer being my favorite since she is mothering and he is child innocence.**

 **Also, I will be switching Point of View, but it will be easy to tell who's it is by context.**

 **Thank you all again. I hope you enjoyed.**


	2. Chapter 2

" _ **The worst type of crying wasn't the kind everyone could see- the wailing on the street corners, the tearing at clothes. No, the worst kind happened when your soul wept and no matter what you did, there was no way to comfort it. A section withered and became a scar on the part of your soul that survived."**_

 _ **~Katie McGarry**_

* * *

 _Bubbles Utonium… The youngest out of three superhero sisters. The baby. The sweet one. The one who couldn't harm a fly. However, no one, but Mojo, The Professor, or my sisters remembered when I completely lost it and became hard core. Honestly, I don't remember all of it. It was like something that just broke out. A monster of some sort. I was a prisoner in my own body…_

 _Bloss, do you remember when I screamed from my nightmares. I would wake up in a cold sweat. My PJ's would be soaked. My hair would stick to my forehead. Inside my chest, my heart would race and threaten to jump out. My stomach would twist and I swear I was close to throwing up. I did bad things in my nightmares._

 _But all you had to do was place a hand on my shoulder and I would instantly calm down. I would crash into your chest and sob. You cuddled me, rubbing small circles on my back until I fell asleep. I would wake to smell pancakes and rush downstairs where you had my plate ready with a smiley face drawn with whip cream._

 _How do I say thank you for everything? More importantly… How do I keep the monster inside without you to tame it…?_

"Let me go, Buttercup!" I screamed and kicked. "Let me go! Blossom! Blossom! Blossom!" I continued to scream. I flung myself around trying to break free from Buttercup's grasp. I had to get my sister back. My big sister that I loved with all my heart.

Buttercup never lightened her grip. If anything, it only got stronger.

"Bubbles you're lucky this room is soundproof. Blossom would be upset with you."

"Let her! Let her come down to scold me! I want Blossom! Blossom! Blossom!"

"Bubbles! Knock it off! Get yourself together!"

I was about to scream again but then I felt a vibration beneath my feet. Buttercup and I tumbled to the floor as it knocked us around. A giant boom sounded from a distance. A sick feeling came to me. My eyes widened when I realized what that could mean…

Buttercup finally let me go because she knew too. Her skin was now pale and her eyes glossed over. A pain shot through my heart and I'm sure Buttercup was feeling the same.

"Blossom!" I screamed.

* * *

 _Three Days Prior_

I hummed to myself as I gazed in my vanity mirror. I reached up and uncurled my pigtails. I smiled brightly when I saw them bounce into my place. Then I continued the rest of my morning rituals on Saturdays. My humming continued as I heard footsteps in the hall. Buttercup must be awake.

Today I was excited. No nightmare last night. And today I was going to go on a Date with Boomer! So far, so amazing. My skin was looking smooth and clean. No bags under my eyes, and today I feel good. A perfect day to have a date with a perfect boy.

I giggled to myself. I was so wrapped in thought that I didn't notice Blossom come into my room.

"Good morning." She greeted. I turned around in my spot and smiled at her. She approached me with a glass of orange juice, also a Saturday tradition. She kissed my temple as I took a drink. Then she turned and picked up some trash I laid nearby.

"Good Morning, Blossy. What do you have planned today?" She hummed in thought and then gave me a smile.

"Nothing as exciting as you have planned." I blushed and she laughed. "Just make sure you're home by six. Boomer can stay here as long as he wants but you need to be home by dinner." She said. I nodded and looked back at the mirror.

Today was going to be a good day. I could feel it.

Boomer came to my house around one and we left about thirty minute later. He loves to talk to Blossom before he leaves. He wants her to think he's responsible and such. Which he is but he loves her approval. Blossom is much more open about appraisal than Brick so Boomer craves it.

Buttercup gave him a nod and he was over the moon. I love That he loves my family so much. It makes my heart smile.

We ended up going to the mall for the first part and eating in the food court. He talked about his upcoming photography project. He wanted me to come along so that we could sight see some of the places he had to get pictures of. Of course, I agreed. I love going so I can sketch some of the places myself.

Then we went into the arcade. I used to avoid the place. Especially after Buttercup forced me to participate in laser tag. It was fun and all, but the darkness and the noises gave me a small panic attack. However, Boomer makes it fun for me. He even lets me chose most of the games and lets me keep all the tickets so I can get the prizes.

He's just the sweetest.

Then we flew to the museum, but we weren't able to go in because it looked as someone had broken in. The Police was everywhere and the caution tape kept people at a far distance. I could see Ms. Bellum and the Mayor talking at the entrance.

"Mr. Mayor? What happened?" I asked as one of the kind officers let us through. Boomer gazed around concerned at all the artifacts. He came here so much I wouldn't be surprised if he was looking to make sure everything was in the right place.

"Oh, Bubbles! I'm so happy you're here." He approached me. "The alarm went off and one of the security guards were knocked out cold." I gasped softly.

"What was taken?" I asked urgently, ready to find this person and give him a piece of my mind. Art is meant to be shared with the world not taken from it.

"Ah… well We aren't sure." He hung his head. "The roster says all the pieces are here."

"That's why we are on high alert." Ms. Bellum added. "Why go through all the trouble if you don't take anything."

"But they did take something." Boomer spoke from across the hall. We all looked over at him as his eyes stayed focused on one statue, particularly at the statue's hands that were held close to the chest. "This piece used to hold a scroll in the left hands."

"A scroll?" I asked as I flew to him.

"It was said that the artist left a secret message on the scroll but when anyone looked at it was blank. The left arm symbolized being close to the heart."

"A secret message held close to the heart." Ms. Bellum reiterated. "What On earth could that be." Boomer shrugged and looked at her.

"Like I said, those who looked at it said it was blank."

I found myself just staring at the hands of the statue, wondering what could have been so important.

"We'll do some investigating on the matter. Thank you, you two. We appreciate it." Ms. Bellum spoke. Boomer blushed at being acknowledged and I smiled.

"Come one, Boomie. We can go to the park." He nodded and we took off, but I couldn't help but feel a tug at my heart. Something was going to happen… well maybe I was just letting my anxiety get to me.

Around two hours later Buttercup sent me a text message that we were eating at the boys because Blossom was asked to do a special job. It wasn't unusual for Blossom to do certain things on her own, but with the robbery that I saw I felt uneasy. However, I'm a big girl. I can handle anything…

That's what Blossom always says…

 _But I can't escape the screaming in my head and the feel of the cold shackles around my wrists and ankles from the prison within me. Blossom, I need you._

* * *

 **I'm sorry for such a short chapter. The first part of this story will indeed be slow until I can get the ball rolling properly. For now, This will be revolved around Buttercup and Bubbles thoughts, perhaps later I will dedicate some to the boys for their point of views. Thank you for the feedback!**

 **P.S: For those who read And Then You Came Along, I will be updating soon. How soon? Not sure yet. I have a busy week coming up but then I should be free to update. Thank you for your patience.**


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